mdpu-kit takes a system as the data structure. A snapshot of a system is called a frame. A system may contain multiple frames with the same atom types and numbers, i.e. the same formula (like H2O). To contains data with different formulas, one usually needs to divide data into multiple systems, which may sometimes result in sparse-frame systems.
A system should contain system properties, input frame properties, and labeled frame properties. The system property contains the following property:
| ID | Property | Raw file | Required/Optional | Shape | Description |
|---|---|---|---|---|---|
| type | Atom type indexes | type.raw | Required | Natoms | Integers that start with 0. If both the training parameter {ref}type_map <model/type_map> is set and type_map.raw is provided, the system atom type should be mapped to type_map.raw in type.raw and will be mapped to the model atom type when training; otherwise, the system atom type will be always mapped to the model atom type (whether {ref}type_map <model/type_map> is set or not) |
| type_map | Atom type names | type_map.raw | Optional | Ntypes | Atom names that map to atom type, which is unnecessary to be contained in the periodic table. Only works when the training parameter {ref}type_map <model/type_map> is set |
| nopbc | Non-periodic system | nopbc | Optional | 1 | If True, this system is non-periodic; otherwise it's periodic |
The input frame properties contain the following property, the first axis of which is the number of frames:
| ID | Property | Raw file | Unit | Required/Optional | Shape | Description |
|---|---|---|---|---|---|---|
| coord | Atomic coordinates | coord.raw | Å | Required | Nframes * Natoms * 3 | |
| box | Boxes | box.raw | Å | Required if periodic | Nframes * 3 * 3 | in the order XX XY XZ YX YY YZ ZX ZY ZZ |
| fparam | Extra frame parameters | fparam.raw | Any | Optional | Nframes * Any | |
| aparam | Extra atomic parameters | aparam.raw | Any | Optional | Nframes * aparam * Any | |
| numb_copy | Each frame is copied by the numb_copy (int) times |
prob.raw | 1 | Optional | Nframes | Integer; Default is 1 for all frames |
The labeled frame properties are listed as follows, all of which will be used for training if and only if the loss function contains such property:
| ID | Property | Raw file | Unit | Shape | Description |
|---|---|---|---|---|---|
| energy | Frame energies | energy.raw | eV | Nframes | |
| force | Atomic forces | force.raw | eV/Å | Nframes * Natoms * 3 | |
| virial | Frame virial | virial.raw | eV | Nframes * 9 | in the order XX XY XZ YX YY YZ ZX ZY ZZ |
| atom_ener | Atomic energies | atom_ener.raw | eV | Nframes * Natoms | |
| atom_pref | Weights of atomic forces | atom_pref.raw | 1 | Nframes * Natoms | |
| dipole | Frame dipole | dipole.raw | Any | Nframes * 3 | |
| atomic_dipole | Atomic dipole | atomic_dipole.raw | Any | Nframes * Natoms * 3 | |
| polarizability | Frame polarizability | polarizability.raw | Any | Nframes * 9 | in the order XX XY XZ YX YY YZ ZX ZY ZZ |
| atomic_polarizability | Atomic polarizability | atomic_polarizability.raw | Any | Nframes * Natoms * 9 | in the order XX XY XZ YX YY YZ ZX ZY ZZ |
| drdq | Partial derivative of atomic coordinates with respect to generalized coordinates | drdq.raw | 1 | Nframes * Natoms * 3 * Ngen_coords |
In general, we always use the following convention of units:
| Property | Unit |
|---|---|
| Time | ps |
| Length | Å |
| Energy | eV |
| Force | eV/Å |
| Virial | eV |
| Pressure | Bar |